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help > RE: Missing confound-corrected time-series (dsw*.nii) in subject folder
Oct 14, 2021 03:10 AM | Yann Quide
RE: Missing confound-corrected time-series (dsw*.nii) in subject folder
Thanks Alfonso!
The patch worked well, and now my dsw*.nii images are created!
May I ask what was the issue?
Thanks again for your time and help.
Yann
Originally posted by Alfonso Nieto-Castanon:
The patch worked well, and now my dsw*.nii images are created!
May I ask what was the issue?
Thanks again for your time and help.
Yann
Originally posted by Alfonso Nieto-Castanon:
Hi Yann,
Thanks for the detailed info. I think I found the issue, please install the attached patch and re-run denoising and let me know if the dsw*.nii files (finally!) show up. This patch is for release 20b, to install it copy the attached file to your conn distribution folder overwriting the file with the same name there
Best
Alfonso
Originally posted by Yann Quide:
Thanks for the detailed info. I think I found the issue, please install the attached patch and re-run denoising and let me know if the dsw*.nii files (finally!) show up. This patch is for release 20b, to install it copy the attached file to your conn distribution folder overwriting the file with the same name there
Best
Alfonso
Originally posted by Yann Quide:
Hi
Alfonso,
Please find attached the temporalfile.mat after the script stopped.
Thanks for your help.
Yann
Originally posted by Alfonso Nieto-Castanon:
Please find attached the temporalfile.mat after the script stopped.
Thanks for your help.
Yann
Originally posted by Alfonso Nieto-Castanon:
Hi Yann,
Could you please first try typing in Matlab:
conn_process(6)
and selecting to overwrite the existing results, and see if that creates the d*.nii files. If it does not, then please type in Matlab:
dbstop in conn_process.m at 1261
conn_process(6)
and again select to overwrite the existing results. When Matlab stops and the command-line and shows a "K>>" symbol, type:
save temporalfile.mat
and send me the resulting temporalfile.mat file to see if that helps me figure out what might be causing this. If, on the other hand, Matlab does not stop until finished (and shows the normal ">>" symbol instead), then please send me your project conn_*.mat file instead.
Thanks
Alfonso
Originally posted by Yann Quide:
Could you please first try typing in Matlab:
conn_process(6)
and selecting to overwrite the existing results, and see if that creates the d*.nii files. If it does not, then please type in Matlab:
dbstop in conn_process.m at 1261
conn_process(6)
and again select to overwrite the existing results. When Matlab stops and the command-line and shows a "K>>" symbol, type:
save temporalfile.mat
and send me the resulting temporalfile.mat file to see if that helps me figure out what might be causing this. If, on the other hand, Matlab does not stop until finished (and shows the normal ">>" symbol instead), then please send me your project conn_*.mat file instead.
Thanks
Alfonso
Originally posted by Yann Quide:
Dear
Alfonso,
I again tried to re-install the toolbox and restart all preprocessing/denoising steps, making sure all necessary boxes are ticked in setup, DONEWOUTPUTCONFCORR=1, and 'overwrite existing results' is on.
Do you have any suggestion on how I can re-create these missing dsw*.nii files?
I would really appreciate your help on this.
Thanks in advance,
Yann
Originally posted by Yann Quide:
I again tried to re-install the toolbox and restart all preprocessing/denoising steps, making sure all necessary boxes are ticked in setup, DONEWOUTPUTCONFCORR=1, and 'overwrite existing results' is on.
Do you have any suggestion on how I can re-create these missing dsw*.nii files?
I would really appreciate your help on this.
Thanks in advance,
Yann
Originally posted by Yann Quide:
Dear
Alfonso,
I am still having this issue.
I checked all the points you previously raised, but no luck.
I tried to re-install the toolbox etc. still no luck.
Is there a way to re-create these files a posteriori?
Thanks for your help on this.
Best regards,
Yann
Originally posted by Yann Quide:
I am still having this issue.
I checked all the points you previously raised, but no luck.
I tried to re-install the toolbox etc. still no luck.
Is there a way to re-create these files a posteriori?
Thanks for your help on this.
Best regards,
Yann
Originally posted by Yann Quide:
Thanks Alfonso for
your feedback.
I tried to restart the denoising of my data again, making sure all boxes are ticked, checked the conn_process DONEW is set to 1 and overwrite the old data.
But no luck.
Do you think I should try and re-install the toolbox from fresh and re-process my data from scratch?
Or is there an alternative way to create these files?
Thanks again for your help.
Yann
Originally posted by Alfonso Nieto-Castanon:
I tried to restart the denoising of my data again, making sure all boxes are ticked, checked the conn_process DONEW is set to 1 and overwrite the old data.
But no luck.
Do you think I should try and re-install the toolbox from fresh and re-process my data from scratch?
Or is there an alternative way to create these files?
Thanks again for your help.
Yann
Originally posted by Alfonso Nieto-Castanon:
Dear
Yann
That's strange, I would probably suggest double-checking the following:
a) that the 'create cofound-corrected timeseries' option is still checked in the Setup.Options tab
b) that the file conn_process.m in line #1186 has not been modified and the variable DONEW... is set to 1 (it should read:
DONEWOUTPUTCONFCORR=1; % create confound-corrected timeseries option (0: old format -one file per condition-; 1: new format -one file per session-; 2: both)
and c) that when re-running the denoising step you are selecting the option that reads 'overwrite existing results'
With those options the denoised files named d*.nii "should" appear in your subject folders (the file names will only be dsw*.nii if your data was preprocessed in CONN using the default pipeline, otherwise they will simply be named by prepending the letter 'd' to the data in Setup.Functionals (primary dataset)
Hope this helps
Alfonso
Originally posted by Yann Quide:
That's strange, I would probably suggest double-checking the following:
a) that the 'create cofound-corrected timeseries' option is still checked in the Setup.Options tab
b) that the file conn_process.m in line #1186 has not been modified and the variable DONEW... is set to 1 (it should read:
DONEWOUTPUTCONFCORR=1; % create confound-corrected timeseries option (0: old format -one file per condition-; 1: new format -one file per session-; 2: both)
and c) that when re-running the denoising step you are selecting the option that reads 'overwrite existing results'
With those options the denoised files named d*.nii "should" appear in your subject folders (the file names will only be dsw*.nii if your data was preprocessed in CONN using the default pipeline, otherwise they will simply be named by prepending the letter 'd' to the data in Setup.Functionals (primary dataset)
Hope this helps
Alfonso
Originally posted by Yann Quide:
Dear Alfonso and other CONN users,
Although I selected the option to write the confound-corrected time-series in the Setup window, the dsw*.nii files do not appear in my subject folders.
I tried to rerun everything from scratch (including all preprocessing steps just in case), but no luck.
I am using CONN v20b in Matlab 2021a for Windows 10.
Did I miss something?
Is there a way to compute these files a posteriori?
Thanks in advance.
Yann
Although I selected the option to write the confound-corrected time-series in the Setup window, the dsw*.nii files do not appear in my subject folders.
I tried to rerun everything from scratch (including all preprocessing steps just in case), but no luck.
I am using CONN v20b in Matlab 2021a for Windows 10.
Did I miss something?
Is there a way to compute these files a posteriori?
Thanks in advance.
Yann
Threaded View
| Title | Author | Date |
|---|---|---|
| Yann Quide | Aug 31, 2021 | |
| Alfonso Nieto-Castanon | Sep 15, 2021 | |
| Yann Quide | Sep 16, 2021 | |
| Yann Quide | Oct 11, 2021 | |
| Yann Quide | Oct 13, 2021 | |
| Alfonso Nieto-Castanon | Oct 13, 2021 | |
| Yann Quide | Oct 13, 2021 | |
| Alfonso Nieto-Castanon | Oct 13, 2021 | |
| Yann Quide | Oct 14, 2021 | |
| Alfonso Nieto-Castanon | Oct 14, 2021 | |
| Yann Quide | Sep 13, 2021 | |